A comparison of both stimulus categories suggests that religious thinking is more associated with brain regions that govern emotion, self-representation, and cognitive conflict, while thinking about ordinary facts is more reliant upon memory retrieval networks
They also perceive themselves in a different way than non-believers do. They use a different part of their brain when judging themselves and others. They also use different parts of their brain when imagining God's positive or negative emotions. There are two parts of the brain involved for the task of self-judgment vs. putting oneself into another's mind.
Later in life, the hippocampus shrinks more in born-agains than other believers or in non-believers. This can lead to Alzheimers. Why am I not surprised?